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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgtttctcaaatattttgttgcttcgttaagaatatctgtttagcatgaatttgataggaaccaggataatagttttaaaaactggaaaaaat...

Basic information

species Zea mays
transcript GRMZM2G048804_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048804_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g07100.1 (Oryza sativa), 5'ss of exon 10
ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgtttc-tcaaatattttgttgcttcgttaagaatatctgtttagcatgaa--------tttgataggaaccaggataatagttttaaaaactggaaaaaat
 || || |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||  ||  |||| ||| |||||||||  || |||| ||||||||  ||||   | | |||  | | ||||  | |||| |        | | ||     | | ||| |   |   || |||||| |     
GCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAGgtag--ctatttcatcaaatatagtgttagcttgctaa--acagctgtaaaacatgcaccaaaacatcttattctttcaaagattaacttaacaagaactggga-----
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|31558703|gb|CD527915.1|CD527915
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|33771157|gb|CF272818.1|CF272818
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAA
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAA
EST: gi|94472950|gb|EB701908.1|EB701908
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|12968751|gb|BG265697.1|BG265697
EST:     TTCGACAGAAGTATAAGCCAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTGCAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|113704317|gb|EE681821.1|EE681821
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|37379196|gb|CF626330.1|CF626330
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTTTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|5791304|gb|AI978096.1|AI978096
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|50339821|gb|CO534947.1|CO534947
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|33467111|gb|CF244160.1|CF244160
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|5005582|gb|AI711644.1|AI711644
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|5895669|gb|AW036915.1|AW036915
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|71773196|gb|DR971109.1|DR971109
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|211094046|gb|FL457289.1|FL457289
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAGTATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|74236760|gb|DT644674.1|DT644674
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|211155842|gb|FL114458.1|FL114458
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|32911197|gb|CF016009.1|CF016009
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|24764009|gb|CA399178.1|CA399178
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|78021285|gb|DV489672.1|DV489672
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
EST: gi|113702828|gb|EE680332.1|EE680332
EST:     TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG                         TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT
genomic: TTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 131

ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 148

ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 144

ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 179

ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgt ... cattttgcagTTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAGgtagtgctgtttctcaaatattttgttgcttcgttaagaatatctgtttagcatgaatttgataggaaccaggataatagttttaaaaactggaaaaaat

- - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG